San Francisco 49ers’ loss to Chiefs was a costly one, as Jimmy Garoppolo could be done for the season with an ACL tear

For the San Francisco 49ers, taking a 38-27 loss to the AFC West-leading Kansas City Chiefs on Sunday comes as an afterthought considering what else the team may have lost in the process.

According to head coach Kyle Shanahan, the 49ers fear that starting quarterback Jimmy Garoppolo may have suffered a torn ACL while attempting to lead a fourth-quarter comeback.Along with that, here are five takeaways from the 49ers second loss of the 2018 season

Garoppolo could be done for the year

After taking a big hit near the Chiefs’ nine-yard line midway through the fourth quarter, the 49ers thought Jimmy Garoppolo injured his throwing shoulder as he laid on the ground in the aftermath of his third-down scramble.

Unbeknownst to them, however, Garoppolo’s injury would have the potential to be much worse. The starting quarterback, who signed a $137 million contract this offseason, clutched his left knee while team trainers approached the sideline to provide medical attention.

“With Jimmy [Garoppolo], it was a knee,” Shanahan said. “We’re fearing its an ACL.”

Before Garoppolo took the massive hit from Kansas City defensive back Steven Nelson, the 26-year old signal caller attempted to make a cut using his left leg. As a result of the sharp movement, his knee buckled as the ensuing hit followed.

The 49ers, who were in the midst of an improbable comeback effort after trailing by 28 points in the second quarter, opted to plug in backup C.J. Beathard, who started five games for the 49ers as a rookie in 2017.

“It’s tough. I mean he’s the starting quarterback and a leader on this team,” said Beathard, a 2017 third-round pick out of Iowa. “I’m going to be praying for him and hopefully he can recover and heal up as quickly as possible.”

If, in fact, Garoppolo did tear his ACL, the outlook for the 2018 season will drastically change for the 49ers. A potential playoff appearance — which San Francisco has stated is a goal for the season — may have to wait for 2019 if Garoppolo needs surgery to repair a torn ACL.

Without Garoppolo under center, San Francisco — in the middle of a multi-year rebuild under Shanahan and general manager John Lynch — will be forced to start Beathard, who posted a 1-4 record in his five starts last season.

According to Shanahan, Garoppolo will have an MRI performed on his right knee on Monday to either confirm or rule out a torn ACL.

Richard Sherman injures calf

As if a potentially-season-ending injury to the offensive leader wasn’t enough, defensive leader and team captain Richard Sherman exited Sunday’s game against Kansas City late in the first half with what was later revealed to be a calf injury.

“It was from his calf to his heel,” Shanahan said on Sunday. “Same stuff that was bothering him going into [the game].”

Given the fact that Sherman has had surgery on each Achilles heel — one to repair a tear, the other to clean out bone spurs — in the last 10 months, this is potentially very worrying.

According to Chris Biderman of the Sacramento Bee, Sherman was spotted leaving the locker room in Kansas City with a walking boot.

Sherman will undergo an MRI on the heel/calf area on Monday, similar to Garoppolo to check the severity of the injury.

Sherman did return to the 49ers sideline in the second half but did not re-enter the game.

A lengthy Sherman absence is one San Francisco can ill afford. Safety Jaquiski Tartt didn’t practice for two days this week and was questionable headed into Sunday. Adrian Colbert dealt with a shoulder injury in Week 2, as did Tartt, and K’Waun Williams was limited in Week 2 because of a hip issue.

In the wake of Sherman’s exit, the 49ers put second-year cornerback Ahkello Witherspoon in his place after benching the Colorado product to begin the game. Witherspoon, too, has had to deal with health issues, negotiating an ankle problem last week.

Penalties are killing the 49ers

The 49ers were flagged 14 times for 147 yards.

In the first half alone, San Francisco was flagged eight times for 91 yards, including a defensive pass interference call in the second quarter that resulted in a 31-yard penalty.

The 49ers also set up Kansas City at their one-yard line, which led to a 1-yard touchdown run by Chiefs running back Kareem Hunt.

A crucial offensive flag halted a comeback effort late in the fourth quarter. With 5:27 left in the game, Beathard, who had just entered for the injured Garoppolo, threw what looked to be a touchdown strike to tight end George Kittle.

The play was called back due to a questionable offensive pass interference call against fullback Kyle Juszczyk, who made contact with his defender near the play.

“I was shocked [at the flag],” Shanahan admitted. “I thought we were going to get a call there so I was real surprised our fullback [Juszczyk] got a call of offensive PI.”

With 14 flags in Week 3, the 49ers are now in a four-way tie with the Denver Broncos, Jacksonville Jaguars and Green Bay Packers as the third-most penalized team in the NFL with 26.

49ers able to make halftime adjustments

Trailing by 25 points at the half, the San Francisco had to change something if it hoped to keep from being embarrassed on the road.

Up until that point, the 49ers looked lethargic and unprepared on both sides of the ball as Kansas City dominated the first 30 minutes of play.

Offensively, the 49ers found little success, only scoring 10 points and punting on four of their first six possessions.

On the defensive side of things, Kansas City’s screen game gave defensive coordinator Robert Saleh’s group fits, and keeping second-year quarterback Pat Mahomes contained looked impossible.

Once the second half started, though, the 49ers 14 unanswered points in the third quarter, turning a blowout into a competitive affair.

“I just thought we got on a roll better,” said Shanahan. “We just got in a better rhythm. When you start moving the chains, you stay out on the field for a little bit longer. Got going on offense and that kept the defense off of the field.”

While San Francisco’s offense picked up the pace, the defense began to settle in as well, holding the Chiefs to only three points in the second half.

They were also able to limit the Chiefs to 105 total yards after halftime, compared to 279 yards in the first two quarters of play.

Keep on running

The one things that remained consistent throughout the 49ers’ first two regular season games has been their ability to run the ball.

Week 3 was no different, as San Francisco piled on 178 total rushing yards against Kansas City.

Led by Alfred Morris, who had 90 yards and a touchdown on only 10 carries, the 49ers’ ability to rush the ball was one of the primary reasons they were able to turn the game around in the second half.

Of the 222 yards gained in the second half, 104 came on the ground from Morris and second-year back Matt Breida.

By running the ball so successfully, the 49ers were able to keep the Chiefs’ defense honest, opening up the play-action pass.

If Garoppolo is indeed out for the season, San Francisco’s running game will be that much more important if they hope to squeeze out a few more wins.